There is considerable interest in mining neuroimage data to discover clinically meaningful connectivity patterns to inform an understanding of neurological and neuropsychiatrie disorders. Subgraph mining models have been used to discover connected subgraph patterns. However, it is difficult to capture the complicated interplay among patterns. As a result, classification performance based on these results may not be satisfactory. To address this issue, we propose to learn non-linear representations of brain connectivity patterns from deep learning architectures. This is non-trivial, due to the limited subjects and the high costs of acquiring the data. Fortunately, auxiliary information from multiple side views such as clinical, serologic, immunologic, cognitive and other diagnostic testing also characterizes the states of subjects from different perspectives. In this paper, we present a novel Multi-side-View guided AutoEncoder (MVAE) that incorporates multiple side views into the process of deep learning to tackle the bias in the construction of connectivity patterns caused by the scarce clinical data. Extensive experiments show that MVAE not only captures discriminative connectivity patterns for classification, but also discovers meaningful information for clinical interpretation.